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The refund counter in TurboTax has a lot going on there and is not accurate until it has all of the information entered. It could be something else that has made it make that change in your refund counter that didn't get calculated until after you finished entering the 109-R.
That said, the first thing to make sure is that the code on your 1099-R in box 7 is a G for a non-taxable rollover and that the amount in box 2 is zero. If either of these is not the case then the rollover may be considered partially taxable.
What did you transfer it from? Did you roll it into a regular 401K or a ROTH 401K ? What code is in box 7?
Also, is the IRA/SEP/SIMPLE box marked?
Does box 2a show a nonzero amount
To help clarify your question and so we can give a more helpful answer: How was your Form 1099-R coded in Box 7? Does Box 2a have an amount? Is the Box checked for IRA/SEP/SIMPLE?
Click here for a description of the Codes for Box 7 of Form 1099-R.
Click here for where to enter your Form 1099-R
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